CRISPR-Combo–mediated orthogonal genome editing and transcriptional activation for plant breeding

Changtian Pan, Yiping Qi

Published: 2023-04-20 DOI: 10.1038/s41596-023-00823-w

CRISPR-Combo

orthogonal genome editing

transcriptional activation

plant breeding

Cas9

AI 解读

Self-assembled ultraflexible probes for long-term neural recordings and neuromodulation

iDRiP for the systematic discovery of proteins bound directly to noncoding RNA

A robust unsupervised machine-learning method to quantify the morphological heterogeneity of cells and nuclei

Spooling electrochemiluminescence spectroscopy: development, applications and beyond

Acoustic tweezers for high-throughput single-cell analysis

A flow cytometry-based protocol for syngenic isolation of neurovascular unit cells from mouse and human tissues

An integrated pipeline for comprehensive analysis of immune cells in human brain tumor clinical samples

Purification and functional characterization of novel human skeletal stem cell lineages

Automated human induced pluripotent stem cell culture and sample preparation for 3D live-cell microscopy

Detect-seq, a chemical labeling and biotin pull-down approach for the unbiased and genome-wide off-target evaluation of programmable cytosine base editors

查看全部

Sections

Figures

References

CRISPR–Cas nuclease systems, base editors, and CRISPR activation have greatly advanced plant genome engineering. However, the combinatorial approaches for multiplexed orthogonal genome editing and transcriptional regulation were previously unexploited in
Introduction
Materials
Procedure
Troubleshooting
Timing
Anticipated results
References
ACKNOWLEDGMENTS

Gasiunas, G., Barrangou, R., Horvath, P. & Siksnys, V. Cas9-crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria. Proc. Natl Acad. Sci. USA 109, E2579–E2586 (2012).
Jinek, M. et al. A Programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337, 816–821 (2012).
Gao, C. Genome engineering for crop improvement and future agriculture. Cell 184, 1621–1635 (2021).
Doudna, J. A. & Charpentier, E. Genome editing. The new frontier of genome engineering with CRISPR-Cas9. Science 346, 1258096 (2014).
Jiang, F. et al. Structures of a CRISPR-Cas9 R-loop complex primed for DNA cleavage. Science 351, 863–867 (2016).
Weiss, T. et al. Epigenetic features drastically impact CRISPR–Cas9 efficacy in plants. Plant Physiol. 190, 1153–1164 (2022).
Zhu, X. et al. Cryo-EM structures reveal coordinated domain motions that govern DNA cleavage by Cas9. Nat. Struct. Mol. Biol. 26, 679–685 (2019).
Ran, F. A. et al. Genome engineering using the CRISPR-Cas9 system. Nat. Protoc. 8, 2281–2308 (2013).
Feldman, D. et al. Optical pooled screens in human cells. Cell 179, 787–799.e17 (2019).
Lu, Y. et al. Genome-wide targeted mutagenesis in rice using the CRISPR/Cas9 system. Mol. Plant 10, 1242–1245 (2017).
Meng, X. et al. Construction of a genome-wide mutant library in rice using CRISPR/Cas9. Mol. Plant 10, 1238–1241 (2017).
Komor, A. C., Kim, Y. B., Packer, M. S., Zuris, J. A. & Liu, D. R. Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage. Nature 533, 420–424 (2016).
Gaudelli, N. M. et al. Programmable base editing of A•T to G•C in genomic DNA without DNA cleavage. Nature 551, 464–471 (2017).
Huang, T. P., Newby, G. A. & Liu, D. R. Precision genome editing using cytosine and adenine base editors in mammalian cells. Nat. Protoc. 16, 1089–1128 (2021).
Molla, K. A., Sretenovic, S., Bansal, K. C. & Qi, Y. Precise plant genome editing using base editors and prime editors. Nat. Plants 7, 1166–1187 (2021).
Maeder, M. L. et al. CRISPR RNA-guided activation of endogenous human genes. Nat. Methods 10, 977–979 (2013).
Qi, L. S. et al. Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell 152, 1173–1183 (2013).
Konermann, S. et al. Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex. Nature 517, 583–588 (2015).
Pan, C., Sretenovic, S. & Qi, Y. CRISPR/dCas-mediated transcriptional and epigenetic regulation in plants. Curr. Opin. Plant Biol. 60, 101980 (2021).
Pan, C. et al. CRISPR–Act3.0 for highly efficient multiplexed gene activation in plants. Nat. Plants 7, 942–953 (2021).
Zhang, Y., Malzahn, A. A., Sretenovic, S. & Qi, Y. The emerging and uncultivated potential of CRISPR technology in plant science. Nat. Plants 5, 778–794 (2019).
Joung, J. et al. Genome-scale CRISPR-Cas9 knockout and transcriptional activation screening. Nat. Protoc. 12, 828–863 (2017).
Adli, M. The CRISPR tool kit for genome editing and beyond. Nat. Commun. 9, 1911 (2018).
Pan, C. et al. Boosting plant genome editing with a versatile CRISPR-Combo system. Nat. Plants 8, 513–525 (2022).
Kiani, S. et al. Cas9 gRNA engineering for genome editing, activation and repression. Nat. Methods 12, 1051–1054 (2015).
Breinig, M. et al. Multiplexed orthogonal genome editing and transcriptional activation by Cas12a. Nat. Methods 16, 51–54 (2019).
Ren, Q. et al. Improved plant cytosine base editors with high editing activity, purity, and specificity. Plant Biotechnol. J. 19, 2052–2068 (2021).
Atkins, P. A. & Voytas, D. F. Overcoming bottlenecks in plant gene editing. Curr. Opin. Plant Biol. 54, 79–84 (2020).
Horlbeck, M. A. et al. Nucleosomes impede Cas9 access to DNA in vivo and in vitro. Elife 5, e12677 (2016).
Khanday, I., Santos-Medellín, C. & Sundaresan, V. Rice embryogenic trigger BABY BOOM1 promotes somatic embryogenesis by upregulation of auxin biosynthesis genes. N. Phytol. 238, 673–687 (2020).
Shen, J. P. et al. Combinatorial CRISPR-Cas9 screens for de novo mapping of genetic interactions. Nat. Methods 14, 573–576 (2017).
Boettcher, M. et al. Dual gene activation and knockout screen reveals directional dependencies in genetic networks. Nat. Biotechnol. 36, 170–178 (2018).
Branzei, D. & Foiani, M. Regulation of DNA repair throughout the cell cycle. Nat. Rev. Mol. Cell Biol. 9, 297–308 (2008).
Debernardi, J. M. & Rowan, B. A. Make it a Combo. Nat. Plants 8, 457–458 (2022).
Nishimasu, H. et al. Engineered CRISPR-Cas9 nuclease with expanded targeting space. Science 361, 1259–1262 (2018).
Walton, R. T., Christie, K. A., Whittaker, M. N. & Kleinstiver, B. P. Unconstrained genome targeting with near-PAMless engineered CRISPR-Cas9 variants. Science 368, 290–296 (2020).
Grünewald, J. et al. A dual-deaminase CRISPR base editor enables concurrent adenine and cytosine editing. Nat. Biotechnol. 38, 861–864 (2020).
Zhang, X. et al. Dual base editor catalyzes both cytosine and adenine base conversions in human cells. Nat. Biotechnol. 38, 856–860 (2020).
Sakata, R. C. et al. Base editors for simultaneous introduction of C-to-T and A-to-G mutations. Nat. Biotechnol. 38, 865–869 (2020).
Li, C. et al. Targeted, random mutagenesis of plant genes with dual cytosine and adenine base editors. Nat. Biotechnol. 38, 875–882 (2020).
Li, C. et al. SWISS: multiplexed orthogonal genome editing in plants with a Cas9 nickase and engineered CRISPR RNA scaffolds. Genome Biol. 21, 141 (2020).
Esvelt, K. M. et al. Orthogonal Cas9 proteins for RNA-guided gene regulation and editing. Nat. Methods 10, 1116–1123 (2013).
Boutilier, K. et al. Ectopic expression of BABY BOOM triggers a conversion from vegetative to embryonic growth. Plant Cell 14, 1737–1749 (2002).
Zuo, J., Niu, Q. W., Frugis, G. & Chua, N. H. The WUSCHEL gene promotes vegetative-to-embryonic transition in Arabidopsis. Plant J. 30, 349–359 (2002).
Debernardi, J. M. et al. A GRF–GIF chimeric protein improves the regeneration efficiency of transgenic plants. Nat. Biotechnol. 38, 1274–1279 (2020).
Qiu, F. et al. Transient expression of a TaGRF4-TaGIF1 complex stimulates wheat regeneration and improves genome editing. Sci. China Life Sci. 65, 731–738 (2022).
Dong, C., Fontana, J., Patel, A., Carothers, J. M. & Zalatan, J. G. Synthetic CRISPR-Cas gene activators for transcriptional reprogramming in bacteria. Nat. Commun. 9, 2489 (2018).
Fontana, J. et al. Effective CRISPRa-mediated control of gene expression in bacteria must overcome strict target site requirements. Nat. Commun. 11, 1–11 (2020).
Li, Z. et al. A potent Cas9-derived gene activator for plant and mammalian cells. Nat. Plants 3, 930–936 (2017).
Huminiecki, Ł. & Horbańczuk, J. Can we predict gene expression by understanding proximal promoter architecture? Trends Biotechnol. 35, 530–546 (2017).
Lai, H. Y. et al. iProEP: a computational predictor for predicting promoter. Mol. Ther. Nucleic Acids 17, 337–346 (2019).
Umarov, R., Kuwahara, H., Li, Y., Gao, X. & Solovyev, V. Promoter analysis and prediction in the human genome using sequence-based deep learning models. Bioinformatics 35, 2730–2737 (2019).
Shahmuradov, I. A., Umarov, R. K. & Solovyev, V. V. TSSPlant: a new tool for prediction of plant Pol II promoters. Nucleic Acids Res. 45, e65 (2017).
Chavez, A. et al. Comparison of Cas9 activators in multiple species. Nat. Methods 13, 563–567 (2016).
Manghwar, H. et al. CRISPR/Cas systems in genome editing: methodologies and tools for sgRNA design, off-target evaluation, and strategies to mitigate off-target effects. Adv. Sci. 7, 1902312 (2020).
Liu, H. et al. CRISPR-P 2.0: an improved CRISPR-Cas9 tool for genome editing in plants. Mol. Plant 10, 530–532 (2017).
Chuai, G. H., Wang, Q. L. & Liu, Q. In silico meets in vivo: towards computational CRISPR-based sgRNA design. Trends Biotechnol. 35, 12–21 (2017).
Wang, Z. P. et al. Egg cell-specific promoter-controlled CRISPR/Cas9 efficiently generates homozygous mutants for multiple target genes in Arabidopsis in a single generation. Genome Biol. 16, 144 (2015).
Lee, K. et al. Activities and specificities of CRISPR/Cas9 and Cas12a nucleases for targeted mutagenesis in maize. Plant Biotechnol. J. 17, 362–372 (2019).
Wang, X. et al. Efficient base editing in methylated regions with a human apobec3a-cas9 fusion. Nat. Biotechnol. 36, 946–949 (2018).
Wu, Y. et al. CRISPR-BETS: a base-editing design tool for generating stop codons. Plant Biotechnol. J. 20, 499–510 (2022).
Goodstein, D. M. et al. Phytozome: a comparative platform for green plant genomics. Nucleic Acids Res. 40, D1178–D1186 (2012).
Cui, Y., Xu, J., Cheng, M., Liao, X. & Peng, S. Review of CRISPR/Cas9 sgRNA design tools. Interdiscip. Sci. 10, 455–465 (2018).
Blin, K., Shaw, S., Tong, Y. & Weber, T. Designing sgRNAs for CRISPR-BEST base editing applications with CRISPy-web 2.0. Synth. Syst. Biotechnol. 5, 99–102 (2020).
Hwang, G.-H. et al. Web-based design and analysis tools for CRISPR base editing. BMC Bioinformatics 19, 542 (2018).
Bae, S., Park, J. & Kim, J. S. Cas-OFFinder: a fast and versatile algorithm that searches for potential off-target sites of Cas9 RNA-guided endonucleases. Bioinformatics 30, 1473–1475 (2014).
Ren, Q. et al. PAM-less plant genome editing using a CRISPR–SpRY toolbox. Nat. Plants 7, 25–33 (2021).
Billon, P. et al. CRISPR-mediated base editing enables efficient disruption of eukaryotic genes through induction of STOP codons. Mol. Cell 67, 1068–1079.e4 (2017).
Labun, K., Montague, T. G., Gagnon, J. A., Thyme, S. B. & Valen, E. CHOPCHOP v2: a web tool for the next generation of CRISPR genome engineering. Nucleic Acids Res. 44, W272–W276 (2016).
Liu, H. et al. CRISPR-ERA: a comprehensive design tool for CRISPR-mediated gene editing, repression and activation. Bioinformatics 31, 3676–3678 (2015).
Gong, X., Zhang, T., Xing, J., Wang, R. & Zhao, Y. Positional effects on efficiency of CRISPR/Cas9-based transcriptional activation in rice plants. aBIOTECH 1, 1–5 (2020).
Pan, C. & Qi, Y. CRISPR-Act3.0-based highly efficient multiplexed gene activation in plants. Curr. Protoc. 2, e365 (2022).
Cong, L. et al. Multiplex genome engineering using CRISPR/Cas systems. Science 339, 819–823 (2013).
Zhang, X., Henriques, R., Lin, S. S., Niu, Q. W. & Chua, N. H. Agrobacterium-mediated transformation of Arabidopsis thaliana using the floral dip method. Nat. Protoc. 1, 641–646 (2006).
Wang, K. (ed.) Agrobacterium Protocols Vol. 1 (Humana Press, 2006).
Liu, Q. et al. Hi-TOM: a platform for high-throughput tracking of mutations induced by CRISPR/Cas systems. Sci. China Life Sci. 62, 1–7 (2019).
Clement, K. et al. CRISPResso2 provides accurate and rapid genome editing sequence analysis. Nat. Biotechnol. 37, 224–226 (2019).
Park, J., Lim, K., Kim, J. S. & Bae, S. Cas-analyzer: an online tool for assessing genome editing results using NGS data. Bioinformatics 33, 286–288 (2017).
You, Q. et al. CRISPRMatch: an automatic calculation and visualization tool for high-throughput CRISPR genome-editing data analysis. Int. J. Biol. Sci. 14, 858–862 (2018).
Liu, W. et al. DSDecode: a web-based tool for decoding of sequencing chromatograms for genotyping of targeted mutations. Mol. Plant 8, 1431–1433 (2015).
Nishimura, A., Aichi, I. & Matsuoka, M. A protocol for Agrobacterium-mediated transformation in rice. Nat. Protoc. 1, 2796–2802 (2007).
Khanday, I., Skinner, D., Yang, B., Mercier, R. & Sundaresan, V. A male-expressed rice embryogenic trigger redirected for asexual propagation through seeds. Nature 565, 91–95 (2019).
Morgante, M. & Salamini, F. From plant genomics to breeding practice. Curr. Opin. Biotechnol. 14, 214–219 (2003).
Xie, K., Minkenberg, B. & Yang, Y. Boosting CRISPR/Cas9 multiplex editing capability with the endogenous tRNA-processing system. Proc. Natl Acad. Sci. USA 112, 3570–3575 (2015).
Holsters, M. et al. Transfection and transformation of Agrobacterium tumefaciens. Mol. Genet. Genomics 163, 181–187 (1978).
Allen, G. C., Flores-Vergara, M. A., Krasynanski, S., Kumar, S. & Thompson, W. F. A modified protocol for rapid DNA isolation from plant tissues using cetyltrimethylammonium bromide. Nat. Protoc. 1, 2320–2325 (2006).
Liu, Y., Wan, X. & Wang, B. Engineered CRISPRa enables programmable eukaryote-like gene activation in bacteria. Nat. Commun. 10, 3693 (2019).
Fontana, J., Sparkman-Yager, D., Zalatan, J. G. & Carothers, J. M. Challenges and opportunities with CRISPR activation in bacteria for data-driven metabolic engineering. Curr. Opin. Biotechnol. 64, 190–198 (2020).
Ren, X. et al. Enhanced specificity and efficiency of the CRISPR/Cas9 system with optimized sgRNA parameters in Drosophila. Cell Rep. 9, 1151–1162 (2014).
Doench, J. G. et al. Rational design of highly active sgRNAs for CRISPR-Cas9-mediated gene inactivation. Nat. Biotechnol. 32, 1262–1267 (2014).
Wang, T., Wei, J. J., Sabatini, D. M. & Lander, E. S. Genetic screens in human cells using the CRISPR-Cas9 system. Science 343, 80–84 (2014).
Tycko, J., Myer, V. E. & Hsu, P. D. Methods for optimizing CRISPR-Cas9 genome editing specificity. Mol. Cell 63, 355–370 (2016).
Liu, G., Yin, K., Zhang, Q., Gao, C. & Qiu, J. L. Modulating chromatin accessibility by transactivation and targeting proximal dsgRNAs enhances Cas9 editing efficiency in vivo. Genome Biol. 20, 145 (2019).
Verkuijl, S. A. & Rots, M. G. The influence of eukaryotic chromatin state on CRISPR–Cas9 editing efficiencies. Curr. Opin. Biotechnol. 55, 68–73 (2019).
Hassan, M. M. et al. Construct design for CRISPR/Cas-based genome editing in plants. Trends Plant Sci. 26, 1133–1152 (2021).
Ma, X., Zhu, Q., Chen, Y. & Liu, Y. G. CRISPR/Cas9 platforms for genome editing in plants: developments and applications. Mol. Plant 9, 961–974 (2016).

CRISPR-Combo–mediated orthogonal genome editing and transcriptional activation for plant breeding

推荐阅读